Single cell analysis of CCRCC patient tumors with respect to normal tissue

Aim of study

The goal of this analysis is to determine if tumor cells expressed ASS1. While it is known that the ASS1 gene is usually shutdown in CCRCC tumors, We posit that some cells may still be expressing ASS1, giving them the ability to metastasis. Wew use a single cell dataset obtained from Young et al.: https://www.science.org/doi/10.1126/science.aat1699

Analysis

Setting up environment

Loading data

Data was downloaded from https://www.science.org/doi/10.1126/science.aat1699

Pre-processing data

There are 3 CCRCC patients, but it seems that something went wrong with the third patient. There is barelly any tumor cells. Thus we remove patient 3 and focus on patient 1 and 2.

Filtering and cleaning data

We follow the classic scanpy tutorial

Plotting the expression of ccRCC markers as well as ASS1 in a UMAP

Normal epithelium, normal immune and normal proximal tubule cells both display homogeneous expression of ASS1 (that is, not all cell express ASS1, but many cells express it and are homogeneously spread across the cell cluster). In contrast, the vast majority of tumor immune cells do not express ASS1. More improtantly, most tumor epithelial cells do not express ASS1, except for a number of tumor cells that clearly displays its expression. This would indicate that a subset of tumor cell have normal levels of expression of ASS1. Some of them seems to be scattered in the cluster with high level of ASS1 expression, while other seems to be more closelly related and have relativelly lower level of expression of ASS1 (compared to the isolated ASS1 expressing cells of the tumor). On the other hand, BCAT1 expression doesn't seem to be well captured in this dataset and is mostly dropped out, as only very few cells overall seesm to show its expression (BCAT1 would be expected to at least be expressed in normal cells).

Tumor cells appear to express more VIM than normal cells. EPAS1 seems to be expressed in specific subsets of normal and tumor cells.

Focus on CCRCC patient 1

Focus on CCRCC patient 2

Focus on CCRCC VHL patient (not many cells sadly)

Violin plot of ASS1 and EPAS1 expression in different cell types

Preparing data for pseudobulked differential analysis

Pseudobulking data

Comparison between tumor and "normal" cells

Progeny anaylsis of tumor vs "normal"

TF activity analysis of tumor vs "normal"

Preparing pseudobulk of ASS1 expressing cancer cells

Differential anylsis between ASS1 cancer cells and other cancer cells